[gmx-users] the growth of the molecule

[Smith, Micholas D.]

I should clarify, If you are not concerned with the formation of covalent bonds, you can simulate growth, to some extent. Protein aggregation, for instance, can be studied with MD because of this; so if you are only interested in the early assembly, and not with electronic structure/covalent bonding, than you are ok. I had interpreted your question to be related to bonding, not just early assembly/aggregation.

As far as adding units at a given time, I don't think gromacs can do that, as it would require your topology to change while the simulation was running (i.e. adding more molecules to your system while it is running). Now you could run multiple simulations of the polyethylene chain at different lengths with a single unit free in solution, and watch how the chain increases, but I don't think you could run a single simulation where you added monomer units on the fly.

-Micholas
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dr. Vitaly Chaban <vvchaban at gmail.com>
Sent: Thursday, September 18, 2014 2:43 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] the growth of the molecule

Why not? Your interaction potential is responsible for everything.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин <saga111a at gmail.com> wrote:
> Can the gromacs simulate the growth of the molecule?
> For example, does it allow to add units to the polymer chain at certain
> times?
> More specifically, it is the increase the chain length of the polyethylene.
>
> Thanks!
> --
> Regards,
> Alexander Selyutin
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